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Related Concept Videos

Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

15.0K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Updated: Mar 28, 2026

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

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Proteogenomics from a bioinformatics angle: A growing field.

Gerben Menschaert1, David Fenyö2

  • 1Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Lab of Bioinformatics and Computational Genomics, Ghent University, Ghent, Belgium.

Mass Spectrometry Reviews
|December 17, 2015
PubMed
Summary
This summary is machine-generated.

Proteogenomics integrates proteomics and genomics using mass spectrometry and sequencing. This review overviews bioinformatics tools essential for advancing genome annotation and understanding proteome complexity.

Keywords:
bioinformaticsgene annotationmass spectrometrynext-generation sequencingproteoformproteogenomicsribosome profiling

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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Area of Science:

  • Proteogenomics
  • Multi-omics research
  • Bioinformatics in life sciences

Background:

  • Proteogenomics combines proteomics and genomics, utilizing mass spectrometry and high-throughput sequencing.
  • Key objectives include refining genome annotation and elucidating proteome complexity.
  • It enables identification of novel proteoforms, transcript isoforms, and sequence variations.

Purpose of the Study:

  • To provide a comprehensive overview of available bioinformatics solutions for proteogenomics research.
  • To highlight tools that aid in genome annotation and proteome complexity analysis.
  • To catalog both standalone and integrated bioinformatics tools for cross-omics studies.

Main Methods:

  • Review of existing literature and bioinformatics tools.
  • Analysis of mass spectrometry and high-throughput sequencing data.
  • Categorization of tools based on their functionality in proteogenomics workflows.

Main Results:

  • A growing number of bioinformatics tools and databases are available for proteogenomics.
  • Tools range from specific step solutions (e.g., custom database building) to complete analysis suites.
  • Some integrative tools are offered as standalone applications, while others are web-based (e.g., Galaxy).

Conclusions:

  • Bioinformatics tools are crucial for streamlining proteogenomics studies.
  • The availability of integrative tools facilitates complete proteogenomics analyses.
  • This review serves as a guide to the current bioinformatics landscape for this evolving field.